High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing
Mostra el registre complet Registre parcial de l'ítem
- dc.contributor.author Lagarde, Julien
- dc.contributor.author Uszczynska-Ratajczak, Barbara
- dc.contributor.author Carbonell, Silvia
- dc.contributor.author Pérez-Lluch, Sílvia
- dc.contributor.author Davis, Carrie A.
- dc.contributor.author Gingeras, Thomas R.
- dc.contributor.author Frankish, Adam
- dc.contributor.author Harrow, Jennifer
- dc.contributor.author Guigó Serra, Roderic
- dc.contributor.author Johnson, Rory
- dc.date.accessioned 2019-04-03T07:34:43Z
- dc.date.available 2019-04-03T07:34:43Z
- dc.date.issued 2017
- dc.description.abstract Accurate annotation of genes and their transcripts is a foundation of genomics, but currently no annotation technique combines throughput and accuracy. As a result, reference gene collections remain incomplete-many gene models are fragmentary, and thousands more remain uncataloged, particularly for long noncoding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture Long Seq (CLS), which combines targeted RNA capture with third-generation long-read sequencing. Here we present an experimental reannotation of the GENCODE intergenic lncRNA populations in matched human and mouse tissues that resulted in novel transcript models for 3,574 and 561 gene loci, respectively. CLS approximately doubled the annotated complexity of targeted loci, outperforming existing short-read techniques. Full-length transcript models produced by CLS enabled us to definitively characterize the genomic features of lncRNAs, including promoter and gene structure, and protein-coding potential. Thus, CLS removes a long-standing bottleneck in transcriptome annotation and generates manual-quality full-length transcript models at high-throughput scales.
- dc.format.mimetype application/pdf
- dc.identifier.citation Lagarde J, Uszczynska-Ratajczak B, Carbonell S, Pérez-Lluch S, Abad A, Davis C, Gingeras TR et al. High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing. Nat Genet. 2017;49(12):1731-40. DOI: 10.1038/ng.3988
- dc.identifier.doi http://dx.doi.org/10.1038/ng.3988
- dc.identifier.issn 1061-4036
- dc.identifier.uri http://hdl.handle.net/10230/37031
- dc.language.iso eng
- dc.publisher Nature Research
- dc.relation.ispartof Nature Genetics. 2017;49(12):1731-40
- dc.rights © Nature Publishing Group. http://dx.doi.org/10.1038/ng.3988
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.subject.keyword Bioinformatics
- dc.subject.keyword Gene expression analysis
- dc.subject.keyword RNA probes
- dc.subject.keyword RNA sequencing
- dc.subject.keyword Sequence annotation
- dc.title High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/acceptedVersion